Omes and Omics

From Omics.org

The word omics refers to a field of study in biology ending in the suffix -omics such as genomics, interactomics, or proteomics. The related ome addresses the objects of study of such fields, such as the genome, interactome, or proteome respectively. Users of the suffix “-om-” frequently take it as referring to totality of some sort and complex networks within the omes.

Origin

The suffix “-om-” originated as a back-formation from “genome”, a word formed in analogy with “chromosome”. The word “chromosome” of course comes from the Greek stems “χρωμ(ατ)-” (colour) and “σωμ(ατ)-” (body). (Thus, had this word been well-formed, it would instead be “chromatosome”.) Because “genome” refers to the complete genetic makeup of an organism, some people have made the inference that there exists some root, *“-ome-”, of Greek origin referring to wholeness or to completion, but such root is unknown to most or all scholars.

Because of the success of large-scale quantitative biology projects such as genome sequencing, the suffix "-om-" has migrated to a host of other contexts. Bioinformaticians and molecular biologists figured amongst the first scientists to start to apply the "-ome" suffix widely.

Omes and Omics people

Bioinformatists and molecular biologists figured amongst the first scientists to start to apply the "-ome" suffix widely. Some early advocates were bioinformatists in Cambridge, UK where there have been many early bioinformatics and omics related labs such as MRC centre, Sanger centre, EBI(European Bioinformatics Institute), Cavendish lab, genetics, and biochemistry departments. For example, MRC centre is where the first genome and proteome projects were carried out. EBI members were some of the earliest bioinformatists. For example, Christos Ouzounis's lab used the term textome. In the mid 1990s, many scientists were not serious about omes and omics trend and jokingly talked about or playfully coined new omes and omics'. While some younger researchers took the terms seriously enough to organize and produce conceptual omes and omics en masse. This trend coupled by the trend of attaching bio- prefix to various biological and programming terms such as Bioperl and Biojava. Jong Bhak was one of the serious early takers of bio-, omes, and omics trend in Cambridge. In USA, George Church lab in Harvard medical school was an advocate of conceptualizing omes and omics as shown in their web pages. In Yale, Mark Gerstein (who received his Ph.D. in MRC centre in Cambridge UK) was active in that trend, too. The historical observation showed one trend. As research scientists increasingly sought to integrate biology with information science, they took up the use of omics. For biologists -omics easily conveyed a key concept, the implications of a complex systems approach, an approach that is closely tied to study of networks, emergent properties and encapsulation concepts of theoretical computer science. Information savvy biologists took up the ideas of Steward Kauffman's work. In 1999 and early 2000s, physicists and computer scientists produced some debatable papers on scale-free network properties in biological systems. These also contributed significantly in the expansion of the use of omics as a way to describe heterogeneous networks of objects.

Acceptance

Some “-ome” other than “genome” are becoming useful. “Proteomics” has become well-established as a term for studying the proteome. Researchers have proposed other “-omes” which are becoming accepted within biology field. Omes and omics concepts provide a distinct knowledge layer for biologists especially when they become interested in high throughput experimental analyses. Modern biology is becoming an information sicence and such omes and omics classification can provide skeletons for various previously less well defined fields. For example, the term genetic study in the past could mean many different things for many different scientists while interactome study clearly sub divides a genetic study to the gene-gene, protein-protein or protein-ligand interactions in terms of large scale information processing to find some networked functional information. Omes and omics is one of the most convenient and extensive reformations of biology since evolution and inheritance concepts were proposed in mid 1800s and molecular sequences and structures were deciphered in 1960s and 1970s. Researchers are taking up the omes and omics very rapidly as shown in the use of the terms in pubmed in the last decade. Some biologists predict that biology will be restructured in the future by omes and omics concepts due to high throughput experimental and information technology.

Pseudo-omics and Nonsensomics

Omics is a progressive and useful concept in biology. It can revolutionize the way biology is done and how we see life in the future. However, omics fields itself is under evolution and natural selection. Some omics do not have livable niche. For example, translationomics does not have any distincive value at the moment while it should correspond to transcriptomics. As time goes by, practically useful omics will survive and go into the mainstream biology while some others will die out until revived in an unexpected way. These unviable omics can be collectively called pseudoomics and nonsensomics.

Some of the new "omes"

The transcriptome, the mRNA complement of an entire organism, tissue type, or cell; with its associated field transcriptomics

The metabolome, the totality of metabolites in an organism; with its associated field metabolomics

The metallome, the totality of metal and metalloid species; with its associated field metallomics

The lipidome, the totality of lipids; with its associated field Lipidomics[3]

The interactome, the totality of the molecular interactions in an organism[4]; a once proposed field of interactomics has generally become known as systems biology

The spliceome (see spliceosome), the totality of the alternative splicing protein isoforms; with its associated field spliceomics.

The ORFeome refers to the totality of DNA sequences that begin with the initiation codon ATG, end with a nonsense codon, and contain no stop codon. Such sequences may therefore encode part or all of a protein.

The speechome. (BBC article on the Speechome Project)

The mechanome refers to the force and mechanical systems at work within an organism.

The Phenome - the organism itself. The Phenome is to the genome what the phenotype is to the genotype.

Note that “comic” does not exemplify this suffix; it derives from Greek “κωμ(ο)-” (merriment) + “-ικ(ο)-” (an adjectival suffix), rather than presenting a truncation of “σωμ(ατ)-”.

Similarly, the word “economy” is assembled from Greek “οικ(ο)-” (household) + “νομ(ο)-” (law or custom), and “economic(s)” from “οικ(ο)-” + “νομ(ο)-” + “-ικ(ο)-”. The suffix -omics is sometimes used to create portmanteau words to refer to schools of economics such as Reaganomics.